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Dealing with strange (and sometimes wrong) CIGARs in alignments #32

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SHuang-Broad opened this issue Oct 9, 2019 · 1 comment
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Dealing with strange (and sometimes wrong) CIGARs in alignments #32

SHuang-Broad opened this issue Oct 9, 2019 · 1 comment
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The strange CIGAR could be something like this in MM2.

Or it could something complained by SortSam from Picard

Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: WARNING: Read name m64020_190419_185501/103416136/ccs, No M or N operator between pair of D operators in CIGAR

when sorting the results of bamout from GATK-HC on a CCS corrected BAM (the source could be MM2).
@SHuang-Broad SHuang-Broad mentioned this issue Oct 15, 2019
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@SHuang-Broad SHuang-Broad self-assigned this Jun 12, 2020
@kvg kvg added the bug Something isn't working label Jun 12, 2020
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kvg commented Jul 13, 2020

Reported to minimap2 repo, but it's not preventing us from doing any work so we shall close this for now.

@kvg kvg closed this as completed Jul 13, 2020
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